AMBER Archive (2004)

Subject: Re: AMBER: amber98 with amberffc+INSIGHT II

From: FyD (
Date: Wed Mar 17 2004 - 09:50:28 CST

Quoting a b <>:

> hi there , i am using amberffc (amber98FF) with insight II.
> when i want to minimize a structure comprised of rna/protein+ligand,
> the amber98 FF does not recognize the atoms of the small molecule
> (ligand). i.e., when i try to assign the potential using
> FF->potentials, it works fine for the biomolecules, but for the ligand i
> get the message "could not assign potential type to <name of atom>" for
> each and every atom in the small molecule.
> i tried for simple molecules, for example NH3 etc. (even from the
> insight library) and it still doesn't work.
> does anybody know what should i do?

Dear t.,

Did you create a topology file for your ligand? It seems not. The amber98.rlb
file converted by AmberFCC provide you topology information for the residues
available in the corresponding AMBER FF library, .i.e. for the regular amino
acids and DNA-RNA nucleotides, and NOT for unusual residues or small organic

So it means you have to create the topology needed for your ligand. By this way,
insightII will recognize your new unit. To build such "rlb" library see:

This means that you have to create a "table" highly similar to an AMBER .prep
file, and add it at the end of the amber98.rlb created by AmberFFC. This table
must contain the same atom names and residue name than those found in your PDB
file (or other format) which contains your protein and ligand.

Best regards, Francois

F.-Y. Dupradeau
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to